BN1504 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 5.4637e-06 3.3647e-03
Layer 4 1.5030e-05 5.1247e-04
Layer 2 9.0390e-05 1.2537e-02
Layer 5 1.3962e-04 9.0991e-04
Layer 6 4.5565e-04 6.1059e-03
Layer 1 3.1796e-03 6.0189e-02
WM 9.9460e-01 4.3568e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
PRNP Expression Distribution
Gene Specificity Score (GSS)
PRNP GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
PRNP Layer 5 2.6426 0.7207
EEF1A2 Layer 5 2.9961 0.7190
PHYHIP Layer 4 2.7188 0.7171
TSC22D1 Layer 2 2.6748 0.7126
CLSTN1 Layer 5 2.9727 0.7106
FAIM2 Layer 5 3.0117 0.7079
APBB1 Layer 4 2.8145 0.7036
BSG Layer 5 2.4883 0.7035
OLFM1 Layer 4 2.5605 0.7021
GRIN1 Layer 4 2.8086 0.7001
TSPYL1 Layer 5 3.0059 0.6982
UBC Layer 2 2.4395 0.6979
CHN1 Layer 5 2.7305 0.6967
LMO4 Layer 4 2.9863 0.6954
GPI Layer 5 2.7852 0.6950
SLC22A17 Layer 5 2.5215 0.6947
CAMK2B Layer 4 2.9805 0.6946
CALM3 Layer 5 2.6484 0.6945
TLE5 Layer 5 2.5605 0.6940
PRKAR1B Layer 5 3.2012 0.6912
ACTB Layer 5 2.4570 0.6900
NEFL Layer 5 2.9922 0.6895
SYN1 Layer 5 3.3574 0.6875
RTN3 Layer 5 2.9023 0.6872
ATP6V0C Layer 5 2.6133 0.6866
CHGA Layer 5 3.1191 0.6861
SNCB Layer 4 2.7275 0.6859
NEUROD2 Layer 5 2.9697 0.6858
HSP90AB1 Layer 5 2.3242 0.6855
NRGN Layer 4 2.3281 0.6852
MORF4L1 Layer 5 2.7656 0.6842
PSAP Layer 4 2.3711 0.6839
THY1 Layer 5 2.7969 0.6833
SIRPA Layer 5 2.6660 0.6826
GNAS Layer 5 2.2969 0.6820
SNRPN Layer 5 2.9668 0.6810
ARL6IP1 Layer 5 3.0859 0.6802
DNM1 Layer 5 2.8906 0.6792
NDRG4 Layer 5 3.0586 0.6790
MEF2C Layer 4 2.8516 0.6786
KIF1A Layer 5 2.6279 0.6785
ATP2B2 Layer 4 2.5391 0.6771
SLC17A7 Layer 5 2.6426 0.6771
WBP2 Layer 5 2.7012 0.6756
TOLLIP Layer 4 2.4512 0.6753
GDI1 Layer 5 2.6367 0.6750
TPI1 Layer 5 2.8086 0.6749
OIP5-AS1 Layer 4 2.5117 0.6739
VSNL1 Layer 5 2.9922 0.6739
APP Layer 5 2.8086 0.6738

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1504
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1504_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1504/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1504/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1504/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1504/report/PD/BN1504_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1504/report/PD/BN1504_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 04:25:46
  • Number of Processes: 10
  • Spending Time: 0h 3m